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Yorodumi- PDB-1sie: MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sie | |||||||||
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Title | MURINE POLYOMAVIRUS COMPLEXED WITH A DISIALYLATED OLIGOSACCHARIDE | |||||||||
Components | POLYOMAVIRUS COAT PROTEIN VP1 | |||||||||
Keywords | VIRUS / COAT PROTEIN / Icosahedral virus | |||||||||
Function / homology | Function and homology information caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | Mouse polyomavirus | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3.65 Å | |||||||||
Authors | Stehle, T. / Harrison, S.C. | |||||||||
Citation | Journal: Structure / Year: 1996 Title: Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments. Authors: Stehle, T. / Harrison, S.C. #1: Journal: To be Published Title: The Structure of Simian Virus 40 Refined at 3.1 Angstroms Resolution Authors: Stehle, T. / Gamblin, S.J. / Yan, Y. / Harrison, S.C. #2: Journal: To be Published Title: Structure Determination of Simian Virus 40 and Murine Polyomavirus by a Combination of 5-Fold and 30-Fold Electron Density Averaging Authors: Yan, Y. / Stehle, T. / Liddington, R.C. / Zhao, H.C. / Harrison, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sie.cif.gz | 426.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sie.ent.gz | 357.5 KB | Display | PDB format |
PDBx/mmJSON format | 1sie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sie_validation.pdf.gz | 973.1 KB | Display | wwPDB validaton report |
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Full document | 1sie_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1sie_validation.xml.gz | 81.1 KB | Display | |
Data in CIF | 1sie_validation.cif.gz | 115 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/1sie ftp://data.pdbj.org/pub/pdb/validation_reports/si/1sie | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | SPACE GROUP I23, A=570 ANG. THERE ARE TWO VIRIONS PER UNIT CELL AND 30 VP1 MONOMERS IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. IN THIS STRUCTURE THERE ARE INVADING ARMS OF SYMMETRY-RELATED NEIGHBORING MONOMERS THAT INVADE THE REFERENCE PENTAMER. IN REFINEMENT, THE AUTHORS USED RESIDUES 337 TO THE C-TERMINUS FROM THE SYMMETRY-RELATED MONOMERS. IN THIS ENTRY, RESIDUES 337 TO THE C-TERMINUS ARE PRESENTED AS THE ACTUAL ARM OF THE MONOMER (THAT INVADES ANOTHER PENTAMER). BECAUSE THE REFINEMENT DID NOT USE A BOND BETWEEN RESIDUES 336 AND 337 (BECAUSE THEY BELONGED TO DIFFERENT CHAINS), THE GEOMETRY OF THAT BOND IS NOT ACCURATE. A STRICT PENTAMER SURROUNDED BY FIVE LOCAL PENTAMERS CONSTITUTES THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. APPLICATION OF THE FIRST FIVE MATRICES TO THE COORDINATE SET GENERATES THAT CRYSTALLOGRAPHIC ASYMMETRIC UNIT. |
-Components
#1: Protein | Mass: 42405.109 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Mouse polyomavirus (strain p16 small-plaque) Genus: Polyomavirus / Species: Murine polyomavirus / Strain: SMALL-PLAQUE P16 / References: UniProt: P49302 #2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.65→12 Å / Num. obs: 244414 / % possible obs: 74 % / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Resolution: 3.65→12 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3.65→12 Å
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